I would skip Osaka, mix Hakone somewhere into your Tokyo stay, and then go Tokyo-Kanazawa-Kyoto-Nagasaki by train and fly back to Haneda to pick up your flight home. Do Osaka and Kobe as day trips from Kyoto if they really appeal. A lot of the temples in Kyoto are best first thing in the morning (both in terms of atmosphere and tourist numbers), which leaves plenty of time to go elsewhere.